Microglial depletion and repopulation reversed CD68+ lysosome size and lipofuscin accumulation in microglia of aged mice. Adult (6–8 weeks old) and aged (16–18 months old) male BALB/c mice were provided diets formulated with vehicle or CSF1R antagonist (PLX5622) for 21 d. After 21 d, all mice were provided vehicle diet for an additional 21 d to allow for repopulation of microglia (Repop). After 21 d of repopulation, CD68 and lipofuscin were assessed in microglia. a Representative confocal images of CD68 and Iba1 immunolabeling in the cortex. b Quantification of microglial CD68+ lysosome size (n = 8 mice/group). c Representative histograms of auto-fluorescence intensity of CD11b+/CD45low microglia by flow cytometry. d Mean fluorescence intensity (MFI) of microglial auto-fluorescence by flow cytometry (n = 14). e Representative confocal images of lipofuscin and Iba1 immunolabeling in the cortex. f Quantification of cortical microglial lipofuscin (n = 8 mice/group). g Representative images of neuronal lipofuscin in the aged brain with and without microglial repopulation. Quantification of neuronal microglial lipofuscin (n = 8 mice/group). h Quantification of neuronal microglial lipofuscin (n = 8 mice/group). Inset shows brain region used for imaging. Scale bars = 25 μm. Bars represent the mean ± SEM. Means with * are different from Adult Control group (P < 0.05), and means with † are different from age-matched controls (P < 0.05).